Investigating the use of portable X-ray fluorescence spectroscopy for rapid quantification of Phosphorus in wheat straw and grains

Gilbert Permalloo

CSIRO Root Architecture & Rhizosphere

Introduction

My name is Gilbert Permalloo. I am a Research Project Officer and I am presently working on roots architecture and rhizosphere of wheat. I worked in sugarcane agronomy for about 24 years and I was doing a little bit of basic programming in Fortran 77 and GWBasic about 30 years ago. Most of my data manipulation and visualisation are done in Excel. I could not write any code in R before I joined Data School and I was spending lots of time working with data in spreadsheets. On the otherhand, I am amazed to witness every day the marvel that R can do with data manipulation and visualisation.

My Project

The aim of this project is to investigate the use of portable X-Ray fluorescense spectrocopy (pXRF) as a rapid method to quantify the amount of phosphorus accumulated in straw and grains. About 200 grab samples were taken from one of three trials for this study. Two large datasets are generated by the pXRF; the chemistry, which is composed of a wide range of chemical elemental composition quantified in ppm, whereas the beamspectra, are spectral values from the X-ray beams. R has been used to clean, tidy and re-organised the data, as well as for graphical display of data. Data for phosphorus have been extracted from the large pXRF generated-dataset and merged with a dataframe that contains unique identification numbers (SampleID) that links the data to the sample source and other tables that contain agronomical data for each sample.

Preliminary results

Some data have been displayed graphically to show any trends

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Tables
Table 1: A table of data
country continent year lifeExp pop gdpPercap
Afghanistan Asia 1952 28.801 8425333 779.4453
Afghanistan Asia 1957 30.332 9240934 820.8530
Afghanistan Asia 1962 31.997 10267083 853.1007
Afghanistan Asia 1967 34.020 11537966 836.1971
Afghanistan Asia 1972 36.088 13079460 739.9811

Fig.1: pXRF instrument used to quantify amount of phosphorus in straw and grains

Plots from R
Amount of phosphorus (ppm) in straw vs in grains

Figure 1: Amount of phosphorus (ppm) in straw vs in grains

Amount of phosphorus in straw and grains vs grain yield

Figure 2: Amount of phosphorus in straw and grains vs grain yield

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My Digital Toolbox

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My time went …

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Next steps

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My Data School Experience

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